[Pipet Users] from Alex Lancaster

J.W. Bizzaro jeff at bioinformatics.org
Sat Jan 6 07:26:42 EST 2001

Below is part of a message I got yesterday...

I was looking at getting involved with Piper, since I like the idea of
pipes for GUIs and multiplexing for CLI...  We do a lot of population
genetic data analysis that involves running various analysis programs
on data, and "piping" it off into different programs, merging results
etc, and also getting into <buzzword>"data mining"</buzzword>.  Due to
time constraints I've been hacking up some godawful shell and awk, but
in the medium-to-long term, Piper, Python and such has to be the way
to go.  So I could act as a beta-tester/bug fixer/guinea pig project
for Piper.  I've been playing around a bit with hacking on GNOME
programs, so I like the idea that you're using GNOME/CORBA as a

Another project you maybe interested in, and is, at least
conceptually, related to Piper, is IMT:


It's a simulation framework in XML that is designed to be a high-level
glue that can bind different simulation frameworks together.  In
essence to provide an abstraction for mixing different layers such as
"R", "Grass" (open source GIS), "GALib" (open source genetic algorithm
library) and "Swarm" (open source discrete event/agent based modelling
toolkit, which is the project I used to be employed to work on before
I went back to grad school).  It's a little different in that it was
inspired more by simulation/modelling issues than bioinformatic/data
analysis, but both IMT and Piper seem, in a broad sense to complement
each other (or at least interoperate).  I haven't worked on IMT, but I
know all the people involved and my former Swarm colleague is working
on the Swarm/IMT integration right on.

Anyway, I mention all of this to give you an idea of my background and
interests.  The holy grail in all this is interoperability and
seamlesness (as much as possible) between data and models in different
knowledge domains, and most genomics/bioinformatics companies doing
any kind of software seem hell-bent to reinvent as many wheels as
possible and create a few Tower's of Babel in the process... 

So that's why the existence of the Open Lab, especially in the gold
rush stampede mentality that so many companies and universities
(sadly) seem to have for genomics these days, is such a vital thing.

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